This work presents the development and implementation of a controller for a wastewater treatment plant with an activated sludge process in an alternate bioreactor and a dynamic settling system. The methodology used is known as Virtual Reference Feedback Tuning, based on the data collection of input and output from the plant to obtain the controller through a defined structure that in this case is specified as a PID controller. The input signals are defined as the Oxygen dilution and the highly degradable Substrate, the output variables considered are the Substrate and the Oxygen.